> Message: 6 > Date: Tue, 19 Oct 2010 09:30:47 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Umbrella sampling with temperature and > pressure coupling method problem > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4cbd9d87.6080...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > chris.ne...@utoronto.ca wrote: > > Use Langevin dynamics (the sd integrator) to control the temperature. > > You are sure to get the correct ensemble that way and if you are doing > > US then you can not extract dynamics anyway. > > > > Hopefully somebody else can address the pressure coupling for you, but > > probably you need to provide more information to get a useful answer > there. > > > > The Berendsen barostat suffers from the same limitations as the thermostat > - the > pressure distribution does not produce a true NPT ensemble. >
Whether the correct canonical ensemble (NPT or NVT) is important (or indispensable) for umbrella sampling? If I used the weak coupling method (Berendsen) to do the simulations, can I extract the PMF from the umbrella sampling simulations? > > -Justin > > > -- original message -- > > > > Dear all, > > > > I want to use umbrella sampling to calculate the PMF of the > > conformational transition of a protein. What temperature coupling method > > and > > pressure coupling method should I use? Berendsen temperature coupling or > > Nose-Hoover temperature coupling? Or each one is OK? > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > >
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